I just tried to import it into excel, but it can only accept a little over a million rows of data. It's 3 columns of data, and all I want to do is graph column 1 against 2 and 3 for two graphs.

I am thinking of making a grid preprocessor which divides the 2D landscape up into cells and marks each cell as having or not having an element within it. There will be a fiddle factor for making the cells small enough to discern information from the graph while large enough to be under 1Million filled cells to fit in excel.

While I do on that or something else, anyone know how to graph all of the data easily?

Why not use a database like SQL or shudder Microsoft Access?
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KronoSMay 28 '13 at 23:25

Lack of knowledge of their existence. I'll try it out.
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SwimBikeRunMay 28 '13 at 23:27

@SwimBikeRun what format are the data in right now?
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nhinkle♦May 28 '13 at 23:40

1

In Excel you can handle more than 1M rows of data in PivotTable and PivotCharts. Go through the import data dialogs - but instead of storing in the Excel sheet in the last step, store it as PivotChart. From here, you can create your chart... Haven't tried with 6M rows, but can imagine that this should work! Good luck!
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Peter AlbertMay 29 '13 at 10:29

2

You should consider methods for aggregating your data. I don't think you'll be able to visually discern 6M rows (or even many less than that). Consider the resolution at which you'll be viewing the data (screen or paper) and that medium's resolution and consider that you can't discern more than one data point to unit of resolution (e.g. dpi or pixel). For example at 1200 dpi, you'd need 5000 inches/417 feet to display 6M datapoints.
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davMay 29 '13 at 12:11

I did this and I am currently waiting on the plot command. It took about 30 seconds to import the data, but I have been waiting two minutes and it still hasn't plotted anything. I did a quick plot of the head of the data, and the plot command is right. How long about should 6 million rows take to plot? More to the point, how do I speed this up? Is there a thinning function for R?
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SwimBikeRunMay 28 '13 at 23:43

@SwimBikeRun, yes momobo has the right idea: take a random sample. I updated my answer.
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PeonMay 29 '13 at 18:12

It's amazing how it is simple to sample in R!
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momoboMay 29 '13 at 21:33

You could also try to sample the data. Take only one in ten (or one in hundert) row und try to plot the result. If your sampling is truly random you should have graph that are pretty much representative of the "population"